Someone's Out to Get You!
by Catygirl
Summary: Jack, Teal'c and Daniel go to visit Sam in Atlantis. Not all is as it seems and it leads to a rollercoaster ride from Pegasus to D.C. NOT part of my other series
1. Chapter 1

Authors Note: First multi-chapter story I wrote. Set during season 4 of Atlantis but not really a crossover as most of it is based on Earth with SG1. This is NOT part of my other series.  
- I am sure that some knowledgable person would be able to tell me what SG1's birthday's are. However for the purpose of this story please just accept the premise given, thanks.  
-The story is written so other chapters will be available soon. I will post probably once a day, I will not demand reviews in order to post but some feedback would be gratefully received.

"Do you really think this is a good idea" Daniel said for at least the tenth time that morning.

Jack appeared to be ignoring him or at least that was what Daniel assumed.

They were in Daniel's lab at the SGC. Daniel was packing the books he felt would be useful during their impromptu visit to Atlantis. Teal'c, who had been the first one packed, was waiting patiently at the door while Jack moved around the lab trying to "encourage" Daniel to pack faster.

"Daniel for crying out loud can you just decide on two books, pick them up and lets go." After more deliberation Daniel put the final book in his pack. He turned thoughtfully and looked at Jack.

"Jack is this a good idea, you know how Sam feels"

"Daniel I am going to say this once and only once, we have not missed an SG1 birthday weekend since we started. That's 11 years Daniel and I'm not missing it this year."

Standing there Daniel realised, perhaps for the first time since Jack had announced the whole plan, that Jack needed to go. It didn't matter what Sam would think- not really, Jack needed to be there.

It had been an original SG1 tradition from the beginning. Daniel and Sam discovered that their birthdays were 2 days apart, although there were a couple of years between them. As a group they had decided to celebrate the two events together. Teal'c didn't have a birthday so Jack decided that Teal'c's birthday would be the day in between. Jack hated celebrating his birthday so effectively the group celebrated all four in the three days.

Through the years they had managed to always be together for their "weekend". None of their prolonged stays "abroad" had interfered and they had always managed to get downtime for the three days. They had even managed it the year Sam was with Pete. It was an original group time. Janet and Cassie hadn't joined in the past and neither Cam nor Vala joined in the last few years.

As Daniel brought his mind back to the present he decided that Sam might be ok with them "appearing" for the three days. In the last few months they hadn't really heard much from her, at least Daniel hadn't. He knew Jack spoke to her as part of her weekly briefings and that Teal'c had met up with her at the SGC on one of her rare trips home but Daniel had been away that week. He realised that he wanted the chance for the four of them to be together

"Ok Jack lets go, but I still think you should have asked her about this"

Jack looked down and away, a look of hurt and a little confusion passing quickly over his face.

"I haven't spoken to her recently" he looked a little sheepish "she's been off world or too busy to continue speaking after the briefing these last few weeks"

Suddenly the activities of the last 24 hours became perfectly clear to Daniel; Jack's snap decision to go to Atlantis and the excuse of the birthday weekend. Jack knew something was wrong and he had decided he could only fix it in person.

As he moved through the corridors towards the Gateroom Daniel developed a nasty feeling in his stomach, usually it was Jack's gut that gave the group direction but Daniel decided that this "weekend" was not going to go well.

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As they stepped through the gate at Midway Jack felt a huge sense of relief. He had hoped to get this opportunity and he had worked hard to pull it off. He had checked the supply dates for Atlantis, with the bridge they now received supplies monthly, he had organised SG1's down time and had badgered the president into letting him review the position of Atlantis instead of Woolsey this time. It had all fallen into place.

The Midway "geeks" were just dialling up Atlantis and Jack was itching to get through. He knew that he would have to keep calm and his emotions in check as he went through; it did not look good for a high ranking airforce officer to run through the gate and sweep the facility commander into a passionate embrace. There was also a part of him that really did not want to see Sam, there was something wrong he could admit that and he was terrified of what it could be.

Daniel. Teal'c and Jack stood waiting for some of the supplies to go through and then followed on. They emerged on Atlantis and looked around, there were people moving the supplies everywhere but no sign of Sam, Major Lorne was in charge.

"General Sir, we had no idea you were coming" Lorne said over the noise, running down the stairs to meet the group and give a quick salute.

"Well it was a spur of the moment decision" Jack stated "we were there, the supplies were going through and we thought we could hitch a ride" Jack said, sounding calm as if this was an everyday occurrence.

He looked around the control room "Where is Col Carter?" he asked trying to sound nonchalant.

"She's in her office Sir" the Major replied "I can take you there"

"Nah I remember the way, thanks Lorne. Teal'c, Danny lets go, we'll check in with Carter then you can be let loose on that library Danny boy"

Jack shot off ahead of both of them. Teal'c moved to keep up with Jack but Daniel decided to take his time.

He wasn't quite sure what happened next.

One minute he was meandering up the stairs, the next Jack was pushing back down the stairs with Teal'c following.

"What's going on" Daniel exclaimed.

By now the incoming wormhole had disengaged and Jack was demanding that Midway be dialled immediately. Lorne on the receiving end of the order from someone so high above him did as ordered. The gate dialled and Jack made to go through.

"Daniel Jackson" Teal'c quietly called to him

"I believe it would be wise if I accompany O'Neill and perhaps you could stay and discuss matters with Col. Carter"

"Ok Teal'c but what's going on" Daniel asked still perplexed at the turn of events

"You will discover soon enough Daniel Jackson" Teal'c replied.

With that Teal'c followed Jack though the wormhole. It closed and Daniel made his way to Sam's office.

The sight that was presented to him was enough to stop him in his tracks.

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More soon, I apologise for inconsistancies with Atlantis. Please, if possible, just work with them.


	2. Chapter 2

Authors Note: Thanks for all the reviews. Here is part 2. It's not long but sets up the next section. Oh and because I forgot before - I don't own SG1, but you all know that I'm sure.

Sam didn't really know what was happening. She had been so sad recently. Normally her emotions were kept firmly behind a mask of military toughness that she had learned from her father but today she'd had enough. She had been up for 36 hours straight, complications had arisen with Sheppard and his team on their last mission and having sorted that out she was at the end of her tether.

John Sheppard had arrived in her office and quickly realised that something was wrong. He moved beside her, leaned over and gave her a hug. He'd never done that before and in one of her rare moments of weakness Sam gave in and relaxed into the hug.

She buried her face in his shoulder and immediately began to cry 'what is wrong with me' she thought 'this just isn't me'.

Just as she was pulling back John leaned down and kissed her. She had no idea where it had come from but against her better judgement she kissed back. She was so lonely and Jack didn't matter any more.

A minute or so passed- John was good, not as good as Jack, but good. She vaguely heard the wormhole disengaging for a second time. Part of her mind, the bit that was still rational and functioning, got a little curious. She pulled gently away from John only to see Daniel standing at the door. A look of shock, surprise and hurt on his face.

Flustered Sam moved behind her desk "Daniel what on earth are you doing here?" she asked while beginning to shuffle the papers for something to concentrate on.

Daniel was about to reply when John cleared his throat "Colonel I think I should get back to work if you'll excuse me" he quickly turned at Sam's nod and walked out. "Jackson" he said as he passed Daniel, both a 'hello', 'goodbye' and possibly 'oh crap' all in one.

Once Sheppard had left Daniel turned to Sam "Sam what the hell is going on?" he demanded

Sam looked down; she couldn't meet the eyes of her best friend, not yet. She fussed some more with the papers and finally pulled out the chair. Sitting down she re-asked her question "Daniel why are you here?"

Daniel sat down opposite her, she had forgotten, how could she forget. He answered quietly "It's our birthday weekend, we came to spend it with you, together"

Sam looked at him across her desk, then looked out the door behind him, with a seriously sinking feeling in her stomach "What do you mean "we"" ?

"Jack, Teal'c and I came, Jack organised it……" he was about to continue when Sam jumped in "he's here? Jack's here?" she sat forward in the chair, feeling happy for the 1st time in a long time.

Daniel quickly clarified his statement "they were here Sam, they just left. After Jack came up to find you" he said pointedly

Sam sat back in the chair going over what Daniel had said "but why was he here?" she said aloud, although by the look on her face Daniel could tell she hadn't meant to.

"Sam I know I have just travelled to another galaxy but this is ridiculous. He and we were here to see you. You're our friend and the last time I checked you were Jack's...well... girlfriend" he squirmed over the last word, no-one had really defined what Sam and Jack were. He was beginning to get angry now aswell.

"well you checked wrong Daniel" Sam said with defeat in her voice "Jack and I haven't been together for a month" Sam looked as if she was about to start crying again. Daniel moved round the table, he wasn't going to dispute the statement yet, Sam obviously believed it. Daniel just needed to know details.

"Ok Sam lets go over this one step at a time, cos if you believe that you and Jack have broken up why did he spend most of the morning telling me to get a move on because he was dying to see you. I think we have some seriously crossed wires"

AN: More tomorrow


	3. Chapter 3

Authors Note: Thanks so much for the interest in the story. Hopefully this may answer some of your questions or maybe just pose some more.

Jack was going to go mad, stark raving mad. He was in full "general" flow when Teal'c stepped through the wormhole and Teal'c could see the confrontation brewing.

"Sir, I'm sorry as I said there is a 24 hour layover in Midway when coming from Atlantis" the Sgt in charge stated.

"Of all the stupid most idiotic ideas, who came up with that, was it Mackay. I swear when I get my hands on whoever was involved I will not be responsible….."

"O'Neill" came Teal'c's booming voice. "I believe that the order originated in your office"

Jack stopped mid-rant and turned towards the Sgt, who meekly nodded in response "Sir if you would follow me, I'll take you to the temporary quarters"

The steam went out of Jack quickly and, almost pushed by Teal'c, he followed the Sgt inside the small quarters. Jack sat down on the bed he had a look of complete desolation on his face. Teal'c did not say anything, he simply stood beside the now closed door waiting. They stayed in that position for over 10 minutes. In his mind Jack went over and over what he had seen. He suddenly began to speak

"I was expecting something like this, just came as a bit of a shock, somehow when I pictured this I always imagined it would be Mitchell I was watching"

His statement was both matter of fact and full of despair.

"there was never anything between Col Carter and Col Mitchell O'Neill, you have my word "

Jack looked up at his friend and realised that Teal'c was not just talking about this life but the life SG1 had lived on the Odyssey

"Thanks Teal'c but that situation is a little bit redundant now don't'cha think?"

Jack sat back and tried to plan his next move. He realised that through this whole mess he was going to have to deal with feelings and he really disliked that.

Tealc sat down on the one chair that the room contained and watched as his friends face displayed the emotions going through his mind.

'Right' thought Jack ever the strategist 'might as well peel off the plaster, deal with the feelings, forget it and move on' Jack realistically knew it would be harder than that but he was trying to think optimistically.

Ok Sam is wanting a relationship with someone else, one plaster off. Damn that hurt, he had wanted her for so long and had been so happy in the last two years with their non-defined but very much together relationship.

Second plaster, I need to go back to earth, see the SGC, people at the Pentegon before going to our house in Washington and not blubber like an idiot. That one will be tough, need to make it quick. Walk through the gate, beam to Washington, go straight home. – is it really home now. Maybe I should just pack up and move. So much of Sam is in that house I can't stay there. Right this plaster may need to be accompanied by a large quantity of alcohol.

The third plaster was just too painful that he had to voice it "Teal'c technically I'm their CO, they are breaking the regs. What do I do?"

"What does your heart tell you O'Neill?"

"Honestly, I don't know. There is a huge part of me that wants to punish them, take it out on both of them. But this is Carter, Sam, I just don't think I can do it"

"Then you have your answer O'Neill"

It always amazed Jack how Teal'c saw things in black and white. He was about to say that when there was a commotion outside the door.

Teal'c stepped over and opened it only to come face to face with Sam being restrained by Daniel.

"Daniel, Let Me Go" Sam stated, the unspoken promise that pain would follow if he didn't did not go unnoticed by Daniel.

Jack stood off the bed when he heard her voice. Sam and Jack stared at each other, one with pleading eyes the other with the shutters firmly in place.

All four knew that Jack's sarcastic tongue would come into play and only Daniel was surprised when Jack went straight on the offensive.

"If you've come to ask me not to report you, you can leave, I already made up my mind" keeping his cards close to his chest he did not let on which way his mind had jumped.

Sam who had experienced it all before took it in her stride.

"No Sir" She replied keeping the formality initially.

"I came to speak to Jack" she emphasised his name "we need to clear up some misunderstandings"

Despite being a little taken aback Jack responded "On the contrary Carter I thing everything is clearer now than it has ever been"

She knew he would be stubborn, that he had the right.

"Jack read these please" Sam asked getting to the crux of the issue

Thrown off balance Jack looked down at her hand

"What are they?"

"They're letters from you to me"

Walls now firmly back in place he responded "Carter, I know I can be dense sometimes but I think I know what my letters to you said"

"Jack for crying out loud read the letters or I will read them for you"

"Knock yourself out Carter" he stated as he went back to sit on the bed.

Seeing that there was unlikely to be blood spilt Daniel quietly closed the door and both he and Teal'c waited outside.

Inside Sam began in an unusually quiet voice.

"I'll cut right to the relevant passages" Jack nodded "….There is something I need to tell you. I can't believe it has happened. Sam, I know we said we would wait till after Atlantis before deciding where we were headed but I'm sorry I have met someone else. She is fantastic, she wants kids and is not afraid that her career will take a hit because of them" At this point Sam's voice began to break and Jack sat up straighter, unsure of what he was hearing.

Sam continued "I know this letter will hurt you and believe me I did not want to but I thought it was better you heard from me."

Sam's voice had almost disappeared to a whisper and Jack could tell that she was struggling to hold it together

"Sam I…….." he began to respond

"Wait" she stopped him, "there's more, an e-mail came last week, it was short and too the point 'Sam I know you are faraway but I know that gossip travels far so for the sake of the past I wanted to tell you. The woman I told you about, well she's pregnant. I'm going to be a father again, I'm nervous but very happy. We are going to get married quickly and quietly. I will pack your stuff at the house and send it to the SGC. Good Luck on the mission'"

The emotion she put into the last sentence told Jack everything he didn't know.

"Sam I have no idea what is going on but I swear I never wrote those and there is no pregnant woman, anywhere"

Sam couldn't really decide, given his tone and possible reference to her, if that was all good news. She wiped a stray tear away from her cheek. "I know Daniel filled me in, but I didn't know before"

They both stood in the small space hyper aware of each other but not sure what to do now.

"Are these why you didn't want to speak to me after the IOC briefings?" He asked quietly.

"You didn't want to speak to me" she answered quietly defiant

"We need to sort this out" she added

"Which bit" he responded flippantly.

They both know this was the main point, did they choose to sort them or the crisis. He watched her challenging her to answer.

Before she had the chance Daniel burst into the room throwing apologetic looks at his friends. "I'm sorry but I just realised, I've heard this story before!"

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AN: So I hope we are not all mad at Sam anymore. Typical Daniel takes him a good hour to catch up but what has he remembered. More tomorrow


	4. Chapter 4

Authors Note: Well here is chapter 4. Thanks for all the reviews and feedback, I really enjoy reading them. Hope you enjoy and before you all send me threats I know this doesn't answer many questions it just finishes the Atlantis section for now.

Col John Sheppard could tell when a day was going wrong. In this case, the day was going cataclysmically wrong.

Now standing in the control room, waiting for his CO to return, he had time to reflect on where the day had gone so wrong. Looking back many people would say it was the point where he hugged and then stupidly kissed his CO. But John had higher standards than that, although he acknowledged that recent events would not back that up. He realised that the problem had started when he had seen her on the balcony that morning, she had been so sad; he was always a sucker for an upset woman. Then, instead of watching her, worrying about her and going to her office to see if she was ok, John realised he should have gone and done some sparring with Ronan or bugged Mackay for a while. That was his first mistake, watching her on the balcony, and what a mistake he thought as he reviewed the last few hours events.

So problem number 1, in no real order, he had kissed his CO. Can we all say "Frat Regs" and "Jail time"? What the hell had he been thinking, I mean sure Sam was good looking but he never felt that way about her. It had to have been the tears, women really shouldn't be allowed to cry. Ok he thought after mistake 1, the balcony, there was mistake number 2: Kissing your CO in her open office where anyone can walk in. Leading to problem number 2, her best friend did walk in.

Now John observed, to himself, that ordinarily that would be enough, but no he had to experience problem number 3. Things always come in three's he mused.

A brief word with Major Lorne, after Col Carter and Daniel Jackson left revealed John's biggest problem was also his worst nightmare.

John had realised when he watched Sam that morning that the most obvious reason for her recent sadness was something to do with a man. Although Atlantis was in another galaxy gossip still flowed very well from earth. He knew, therefore that realistically the man in question had to be one of two people, Daniel Jackson who despite problem 2, John was rooting for. The other option didn't bear thinking about. Except he needed to think about it – Major General Jack O'Neill, lets review that rank again Major General.

By now John's heart was beginning to race as the phrase Court Martial was being lit up in neon lights in his brain.

Ok he thought, lets go over this again. I'm kissing Sam, the supplies have arrived, unbeknownst to us three visitors came with the supplies. Lorne had supplied that vital piece of information. O'Neill had gone quickly up to the office with Teal'c and apparently I'm still kissing Sam. O'Neill came back down very quickly and demanded Midway be dialled. Either O'Neill remembered the oven was still on at home or more likely he had seen them kissing. Logically this meant that O'Neill was the one dating Sam, he had got mad and then left without arresting or killing both Sam and well me.

So problem 3 is definitely the biggie then John surmised.

He really wasn't sure where to go from here, in fact he figured there was very little he could do. Sam had followed O'Neill and, depending on how that went, he would either be Court Martialed or …..well…..not.

Excellent well the day could hardly get any worse.

As he thought this the gate began to dial.

"Incoming wormhole" the tech stated.

Mackay walked into the control room, "Are we expecting someone?"

"Not really" John replied "although it is probably Col Carter returning from Midway"

"Why was she at Midway?" asked the ever curious Mackay

"Long story which involves balconies, CO's, windows and ……" he was cut off by Sam stepping through the gate. She had been gone for quite some time.

She greeted the personnel in the gateroom and then called John and Rodney to follow her to her office. Once inside she indicated for them to sit down.

"I'm returning to earth. There is to be a complete review of my command"

There was a stunned silence from both men. John shifted nervously in his seat.

"Eh, Colonel is everything alright?" John asked hoping that would cover the glaringly obvious Courts martial conversation that was sure to follow.

"Yes" she replied "but I need to return to clear up some crossed wires. There are some repercussions from certain events that have occurred recently" Sam stated being deliberately vague due to Rodney's presence.

"I'm back to officially hand command to you both. John you are military commander until I return or another replaces me. Rodney you will deal with the science aspects. No missions are authorised so it's a keep the ship afloat time- quite literally."

By this time Sam had moved around the office and packed her lap-top and a few personal items, she was ready to move to her quarters.

"I'm leaving immediately, I hope to see you soon" her tone dismissed them both.

John hung back "Sam about earlier, I can take some of the blame, it wasn't all you"

"No John, I'm the CO, I take the fall, good luck here I really don't know if I will be back"

With that Sam walked to her quarters, gathered what she needed and headed to the Gate room.

"Dial Midway Sgt" she ordered the tech

"Yes Ma'am"

The gate sprung to life and Sam moved towards the open wormhole. She would miss this place she thought, but there were things that needed sorted on Earth. She took one look back and quickly walked through. Not sure what she would find when she finally reached her destination.


	5. Chapter 5

Authors Note: Here is the next installment. As they are short chapters I decided to give you two. Enjoy

Sgt Walter Harriman had recently found himself looking back wistfully at the good old days. Sure they had often been noted for the constant fear of Goa'uld takeover or Earth's annihilation but he still missed them. Since the defeat of the Ori, Walter felt that the SGC was just not as exciting. Some days a new planet was explored, on others alliances were renewed but it all lacked the sheer pace of earlier years.

However Walter believed things were looking up, if not on the Stargate front definitely on the gossip and betting pools front. It had all began yesterday when Walter had finished cataloguing the Atlantis supplies. A call had come down from the surface telling them that General O'Neill was on his way down. It was not completely unusual for this to happen but the surprised look on General Landry's face had told Walter that the visit was unexpected to say the least. Most people in the control room assumed O'Neill was here to do some snap inspection and so had been taken aback when he only spent 2 minutes with Landry and then went to change into BDU's to visit Daniel.

When the supplies were loaded Walter had been amazed when O'Neill, Jackson and Teal'c came into the Gateroom and started to head through. Walter, doing the only thing he could, quickly contacted Siler to ask for an update on the O'Neill/Carter pools and placed a few strategic bets.

Approximately 10 hours after they had gone through Walter was intrigued to get a message from O'Neill himself on Midway. O'Neill ordered the control room emptied except for Landry and Walter then insisted that they used headphones so their conversations could be private.

The conversation had been disturbing in many ways. At the end Walter had been given orders to find four base personnel. He not only had to find them, but without telling them what was going on, he had to get them to holding cells or quarters with guards posted outside. Walter had now decided that this might be more exciting that a visit from the latest annoyed Goa'uld.

His first port of call was the main check point to see who was on base. He needed to actually go there, not do anything over the phone, O'Neill had insisted.

As he arrived out of the lift he walked over to the check-point.

"Airman, I need to see the sign in book for today"

"Yes sir" the airman looked a little perplexed.

Walter made a few notes on the people he needed

"General's orders, no-one is allowed to sign out until he gives authorisation, understood"

"Yes Sir, is anything wrong"

"Nothing, if anyone gives you a hard time put them on the phone with the General", "Thanks Crawford" Walter added as he made his way back to the lift.

The four personnel were gathered efficiently and without too much hassle by Walter and were now waiting questioning by their superiors.


	6. Chapter 6

Jack was getting jumpy. He needed to be doing something.

Having slept for a time, once Sam had returned, the old SG1 were now all sitting together trying to work through possible scenarios for the mess that existed. This had gone way beyond just trying to break up him and Sam, in fact if what Daniel suspected was true they were only the tip of the iceberg.

They were sitting counting down the last hour before they could leave Midway. The only thing keeping Jack slightly sane was the fact that Sam was here, sure they had lots to work out and had appeared to decide to deal with the crisis first but they were both here. They were sitting on the bottom bed and she had slowly, over the last hour, moved her hand into his. As a rule they didn't do public displays of affection but he needed this. This whole mess was making him nervous, I mean why split up four or five couples, it made no sense.

Daniel was obviously considering the same thing but had moved a little further than Jack in his thought process.

"Sam, how easy would it be for someone to get control of Atlantis" Daniel asked

"I'm not sure what you mean" Sam answered, her brain starting to work through more than the one sentence refrain of 'None of it was true'.

"Well hypothetically if someone wanted to get control of Atlantis, move it so they had complete control and the SGC couldn't reach it, how easy would that be?" Daniel expanded

Sam thought for a moment "Well there are a lot of things to do. If you didn't have lots of your own people and wanted Atlantis personnel to do the job, you would have to get them to believe they were under threat." Sam's mind started to work quicker

"You would want the people to trust you, fake some orders from Earth to get Atlantis to move. Oh you would probably want to destroy Midway as well"

Jack's mind jumped into overdrive at this comment "Wouldn't it be very convenient if Midway was destroyed while the Commander of Atlantis and the Head of Homeworld Security were on board, in this little hypothetical world?"

No-one needed to say anymore. The four of them left the room and Jack pulled rank to get earth dialled. They left Midway without a word, arriving 40 minutes early much to the shock of Walter and Landry.

"Briefing room now" Jack ordered, he assumed Landry would follow the order.

"Walter cut the cameras up there then join us yourself"

Looking down from the control room Walter replied "On it Sir" The excitement seemed to be continuing and Walter for one was very interested in what was going on.

Sitting round the briefing table, Landry at the top as Jack had directed. Jack, Sam and Walter on his right and Daniel and Teal'c on the left.

Jack began the briefing

"So here's what we suspect, for some reason there have been plans made to separate Atlantis from Earth, or at least personnel. We need to interview the four you have locked up"

"I find it hard to believe that they are involved" Landry spoke up

"They're not" Daniel started. Jack glared at him from across the table

"We're not sure how they are connected" Jack concluded.

"After a little discussion on Midway we believe it could have something to do with controlling Atlantis" Sam began

"Right we need to interview them to find out exactly what their stories are, then Colonel Carter and I are off to Washington" Jack added

"Daniel you take Johnstone, Teal'c – Edwards, Sam take Harris and Walter and I will take Wilkins. Lets meet back here in one hour" Jack continued.

The meeting began to break up when Jack spoke again

"Hank can I have a word in your office, I'll be right back Walter"

They both made their way into the office and took a seat.

"Hank I need to ask you something and I need a straight answer" he paused "who has access to personnel mail going from Earth to Atlantis?"

Landry wasn't entirely sure what to make of the question but thought it over.

"Well the mail is sent to the SGC by regular post or internal military mail, depending on the sender. It's sorted by a couple of Corporals in the post room on Level 5. All the Atlantis mail is bagged up and stored in a locked room until supply day.

"Who has access to the room?"

Again Landry thought "The two Corporals, Walter, me, Lieutenant Anderson, the supply master, that's about it, you need a pass code to get in not a swipe card. I suppose anyone who watched someone type it in could access the room"

"Is there one code or several, is it changed regularly?" Jack knew what the procedure had been when he was in charge but that was 3 years ago and things changed.

Hank replied "Two codes, used on different days, no pattern to which code it happens to be"

"Ok that's enough for now" Jack said "Thanks Hank" Jack left a fairly puzzled base commander to follow Walter to interrogation.

Jack could sense that this was going to become more of a nightmare before it was finished. Wiping his fingers through his hair he sighed and headed for the lift.

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AN: If you are a huge Atlantis fan and I am writing something wrong about it please accept apologies from someone who doesn't know as much about the details of how the city works. But I remembered an episode where they moved Atlantis and I figured it would be possible to do that again. Thanks.


	7. Chapter 7

Authors Note: Ok here is number 7. Hope you all enjoy. More tomorrow

Nurse Susan Harris was a little freaked, actually freaked had been a couple of hours ago. Now she was at outright panic. She had spent the last few hours going over all she had done in the days and weeks before.

She had been on duty every day, had seen to all cases assigned to her. She had taken care of SG-11 and 14 when they had post mission check-ups. She was there when Major Hartley died from a primative weapon from a society that didn't welcome visitors, but she couldn't be blamed for that- could she?

This all had to be a mistake.

Susan had just given herself a stern talking to when Colonel Carter walked into the room. She turned, a little surprised,

"Colonel, it's good to see you, I wasn't aware you were back"

Sam sat down at the table across from the nurse. "Susan, I need to ask you some questions, some personal questions"

"Am I in some kind of trouble?" Susan asked quietly

"Lets cover my questions, then I'll answer yours, Susan were you having a relationship with Lieutenant James Dennis?"

"Yes" Susan replied warily "Has something happened, is he alright? Is that why it's you that's here?"

"He's fine" Sam quickly reassured her

"Why did you split up" Sam continued

Susan went a little red "This is private Colonel why do you need to know?"

"Please Susan, tell me the story that you told Daniel a few months ago. I will try to tell you what's going on.

"Okay, when James was transferred to Atlantis with you we didn't think much of it. The bridge was built and General Landry promised us he could come home every month for R and R. Everything was going fine. Then he didn't come back as planned one weekend. I got a note from James brought back by another SF. It said he totally understood why I'd done it and he realised the distance was too much for us. He wished me well. I tried to get the SF to take a note back, but James had told him not to. I put a letter in the next supply package saying I didn't understand and didn't know what I had done but it was returned unopened when Sgt Smith came home a month later. Another letter came saying that James wanted to formally split up and as he was not planning to return to Earth in the near future I should get on with my life"

Listening to the story Sam could still hear the pain in the woman's voice, and how she was struggling not to lose it completely.

"How long had you been together?"

"Well about three years, James was on SG9 until he got orders for Atlantis, you know what it's like Colonel, it's hard to keep a relationship going under these conditions, but we were coping, I thought."

Sam sat back a minute "How do you mean 'I know what it's like'" Her face never gave away the panic she felt that she and Jack had been discovered.

"Sorry Ma'am I didn't mean much, just that people talked about your engagement a few years back. That pressure had broke it off.

"Yes" Sam replied "I know exactly how it is", she paused "have you heard any other stories about this sort of thing happening."

"Well" Susan thought "there was talk of Lieutenant Wilkins having his engagement cancelled, but base gossip didn't confirm why. Conor Johnstone, his girlfriend came back from Atlantis recently but the story was that a parent was sick. Ma'am what is all this about?"

Sam looked at her and knew she had to give her something, even if she herself knew very little.

"We're not sure at the moment, possibly a covert attack on Atlantis. We hope to stop it before anything happens"

"One final thing, how did you normally contact James on Atlantis?"

"Usually e-mail but occasionally written mail. Why?"

"We need to know how people are orchestrating the splits" Sam stated "It seems they have access to both systems at fairly high security level, Thanks for your time, you're free to go now but please don't talk about this interview. We are trying to work under the radar a bit"

"Is that why the cameras have been off all the time?"

"Exactly- thanks"

They both left the room together and Sam ran into Teal'c coming out of his interview.

"How did it go?" she asked

"He was most distressed. He claims to have known that 'something was up' but did not know who to contact to report his feelings"

"Nurse Harris just seemed to accept her relationship was over, I wasn't totally sure how to help her"

"We should return to the briefing room" Teal'c stated. "O'Neill will wish our full reports"


	8. Chapter 8

Authors Note: So chapter 8 is here. Afraid a little angst on the way folks. Sorry. Hope you enjoy, let me know

Jack and Sam boarded the plane for D.C. at around 21:00. Sam hadn't slept well for a long time and Jack was pretty tired. The briefings had taken some time and now, having left their friends in Colorado, they were travelling to D.C. to solve this crisis together, or so Jack had decided. However the problem of a possible attack on Atlantis was the thing furthest from both their minds. Although they had covered some of the personal stuff on Midway, they had completely skipped over the kiss. It was this and the letters that were occupying their minds as they flew across the States.

Deep down Jack accepted Sam had done it because she thought they had split up, but there were other worries in his mind. Like the obvious point that they had served together for 8 years and never once done that. She had been on Atlantis 8 months and was willing to kiss a junior officer. He wasn't sure how to approach that subject. Then there was the root of the whole issue, did they both trust each other enough for this to work if one letter could destroy them? Jack really didn't want to ask that question either.

Sam was in her own world. Most of her was deliriously happy that Jack still wanted her and the letters had not come from him. However she had concerns, like did the real Jack want kids as much as the letter Jack did? Did he really resent her for being in Atlantis and putting her career first? There was a large pit in her stomach that did not want to think about those questions.

So both the Colonel and the General sat on opposite sides of the plane both scared to ask the questions that were slowly eating them alive.

Sam, although she was struggling to relax, finally leaned back and fell asleep about an hour into the flight.

Jack on the other hand went over what needed to be accomplished in D.C. The four interviews had yielded the same results. Three relationships split up, one together because the person came home. Each member of the couples had been told by letter either that the relationship was over because the Atlantis member had found someone else or because they had been told the Earth member had. They then could not reach the other person by letter or email. There were also rumours of at least another three couples who had the same problems.

Jack had been struck by a couple of things during the briefing.

1. How many couples existed at the SGC.

2. Thank goodness no frat regs seemed to have been broken and

3, What on earth was the point in splitting up 8 relationships

Whoever was behind this seemed to have a sick, twisted view of the world. On that thought Jack's brain succumbed to sleep and he was not aware of anything until the pilot announced they were 20 minutes out of Andrews.

Sam was awakened by the announcement. She was feeling slightly rested, if a little confused as to her present location. She was still a little fuzzy as to why they were in Washington, but she was happy to be with Jack. They arrived at Andrews around 2AM and got into a waiting car that took them to Jack's apartment. There they crashed again for a few hours without a great deal of small talk.

After a sleep, shower and breakfast they were both ready to leave for the Pentagon. Jack's car came to pick them up and they were soon stuck in early morning traffic. Desperate to fill the silence that had reigned between them since they had left Midway, Sam started a conversation;

"So how are we going to proceed with the Atlantis problem" Sam asked, hoping she had picked a neutral topic they could discuss easily

Jack looked at her for a few seconds and decided he would just follow her lead. He took a deep breath  
"Well based on the interviews there has obviously been tampering with the mail and e-mail systems. We were the only two who were contacted with fake emails so I also figure someone has to be accessing at least my personal e-mail. As you know it is very high level, so you need to try and solve that one, computers and me don't get on. There's also got to be someone on the mail side, writing the fake letters, but I think I have that figured out"

Sam sat, a little stunned, he had obviously been doing more thinking than her on the plane.

"We need to find out who was behind all of this, it has a familiar slimy ring but I 'm not sure why it would be happening" Jack continued

The traffic began moving and soon the Pentagon was in sight.

Sam was about to ask something else and opened her mouth to do so when Jack cut her off

"Let's just get to my office, we can talk more there" he stated brusquely.

Sam, for the first time since their relationship had got more personal was starting to feel the need to salute and say "Yes Sir". She closed her mouth and turned slightly from him. She went over their interactions since they had woken up that morning. Jack had barely looked at her all morning. Usually when they slept in the same bed they awoke spooned securely together. It had not escaped Sam's notice that Jack had been as far away from her as possible. Taken with the way he had just spoken to her, she began to see that she had been naive to assume everything would go back to normal quickly.

The car pulled up and they both got out, Jack went first as befitted his position but usually he would indicate they should walk side by side, not today.

Sam followed Jack, who was marching through the Pentagon's entrance. Once they cleared initial security they made their way to the SGC/Homeworld Security corridor.

Another airman immediately jumped to attention as Jack walked up

"Sir, Ma'am could you sign here please"

They signed and swiped their ID's before moving onto Jack's office.

The Sgt in the outer office was a little shocked to see her boss, having been told 2 days ago that he would be gone for a week. She took it in her stride and asked

"Would you like coffee or tea, Sir, Ma'am"

Sam looked at Jack who without making eye contact simply replied

"Strong coffee thanks Sgt and hold all my calls except Hammond or the President"

"Yes sir" she replied, and left to get the coffee

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

So we are in DC now, more tomorrow. Oh and if I have the flight times wrong I apologise. I think Colorado is 2 hours behind DC and I figured on a 3 hour trip. Thanks for reading


	9. Chapter 9

Authors Note: Hi there, here is chapter 9. Could I take a moment to thank all reviewers of Chapter 8. There must be a bug in my system as I haven't been able to reply to any of them. Enjoy this short addition to the story. More tomorrow

The plan seemed to be going miraculously well. No-one seemed to know the full extent of what was involved, included his direct followers. He moved from his bed chamber to the plush office area. He thought about everything that his superior mind had put in place. Oh he was in no doubt that O'Neill would figure out parts of what was going on but he suspected it would be too late, it really was now anyway. Everything had fallen into place, exactly as he had foreseen it. He was truly a genius of universal proportions.

The ship, to which he had given this important task, was on it's way. His plant, his eyes and ears, on Atlantis was firmly in place. There was no way anyone would notice that the loyalties of this person were suspect. To finish off a master plan the people who were travelling regularly between Earth and Atlantis had been eliminated.

He would have to admit, a little grudgingly, that it had been a stroke of brilliance. She would need to get a serious reward for that. Usually his style was complete annihilation; mere humans did not matter as long as the job was done. Under normal circumstances he would not have given her idea a second thought, but he had been persuaded to follow her line of thinking. She had pointed out the benefits, in perhaps a forward manner, but her adoration for him had been clear for all to see and now instead of serious complications to his plan he was free from many problems.

Following her plan, but of course his masterful execution, this way had allowed the gradual reduction in contact so that now the only time Earth contacted Atlantis was for the monthly supplies and Atlantis just gave fortnightly reports. That meant a full 2 weeks between contacts. There were no sudden trips home, even using that silly bridge, no calls, e-mails and letters flying between the two bases, and definitely no-one to raise any alarm. He could not have asked for better. The plan would be carried out before Atlantis' next scheduled contact in 11 days. More than enough time to clear odds and ends here on Earth then disappear. He would not be involved in the attack, he really preferred not to get his hands dirty.

As he turned from the elegant wall mirror in which he had been admiring the view, the ball in the middle of the table began to glow.

"My Lord" the face that appeared addressed him "I am pleased to report all is well. We have just crossed into the Pegasus Galaxy and have picked up the transport beacon's signal."

"When will you be in range?"

"We estimate 4 days my Lord"

"You may proceed as planned, you have 12 days by Earth calendar before the plan is finished. Do not fail me by being caught on radar, if you do I will not need to punish you, nothing will be able to save you"

"Yes my Lord"

The transmission ended and the man turned back to the task at hand. Word from the SGC had been quiet in the last 24 hours, it was time to contact his man on the inside. He had long before decided that hiding in plain sight was the easiest way to survive Earth and so he had chosen to keep contact with his subordinates through earthly communication. Although phones were extremely primitive and beneath him, the communication balls were just not easily hidden within top secret military facilities. Therefore he picked up the phone and called the familiar number. His call was placed directly to the extension of the man he needed.

At the SGC Walter picked up the phone.


	10. Chapter 10

Authors Note: Here is chapter 10 - Part 1 of Sam and Jack- The Conversation!!!!! Enjoy

"So" started Sam "what do you know that you are not telling me?" She was standing across from him and feeling as if she should really be doing something. Moreover she usually was more relaxed around Jack but clearly that was not happening today. She hadn't been sure how to start the conversation but knew she had to say something.

Jack looked up from his desk and across to her, his military mask firmly in place.

"About the situation, you mean?"

"Yeah" replied Sam weakly.

Jack sat back in his seat and made Sam feel as if she were in front of the school principal, why was this so difficult, 'because you cheated on him' her very helpful conscious filled in.

"Well obviously someone has access to personal post and e-mail going from Atlantis to Earth."

"Yeah I did figure that bit out" Sam snapped back at him, Jack just glared at her and Sam visibly backed down

"So if we use us as an example, someone had to stop my mail and e-mails getting to you while replacing them with fakes, which reminds me, did you e-mail back or just accept my letters and move on?" He knew by the immediate look of pain on her face that he wasn't being fair but he needed to know.

"I e-mailed back a couple of times before the second e-mail. After that it hurt too much to do anything" she responded quietly

Jack, appearing to ignore her, moved on with the conversation "Ok so e-mail going both ways" continuing he added "there's only one person who could deal with the mail, Landry has him under guard at the SGC"

"So the plan is now to find his boss, yes?" Sam enquired

"Teal'c is working on that as we speak" they shared a look as they each remembered Teal'c interrogation methods.

"Well that should cover the mail, but I'm not sure about the e-mail" Sam concluded, she still found it hard to believe that they hadn't come from Jack. It had to be someone who knew a lot about them and the manner in which Jack would write. Sam zoned back into Jack as he explained further

"That's why we are here, I need you to go over my personal account, see if you can find a hacker or something, have a go anyway"

Jack moved away from behind his desk not looking at Sam and Sam came round. She had very rarely been in his office and when she was she didn't get to see this side of it. She looked at the small photos on the desk, they were so Jack. There was one of Charlie, one of SG1 with Cassie and Janet and finally one of her and Jack taken on a team trip to a hockey game. They had been dating for a few months, she was in Nevada and Daniel and Vala had been 'joined'. She and Jack had decided it was time to let the team in on their personal lives a little.

Sitting in Jack's office, Sam let a small smile cross her face at the memory of her friend's reaction. Teal'c had been unsurprised, Daniel had been happy, Vala had made various inappropriate comments, as she did, and Cam had been in complete shock about the whole thing. It had been a good day.

Jack turned to see Sam looking at the pictures. He could tell which ones she laid her eyes on by the expression on her face. The one of Charlie, her eyes turned a little misty and he could see her pain at never meeting his little boy, the picture of old SG1 gave Sam a small smile as she looked at a young Cassie enjoying herself at the park and then misty again when she saw Janet. Finally her eyes caught the picture of them at the hockey, God he was so in love with her, how could she do this to him, to them?

Sam caught Jack watching her 'he looks so sad' she thought 'I made him get that look, I can be such an idiot sometimes'

"Jack" she started in a whisper

"What is it Carter?" he almost shouted back

"Nothing Sir" she quickly clammed up "I aaahh need your password to log-in"

He looked at her and began to squirm a little "It's astrophysics" he mumbled, "kind of reminds me of someone"

Sam smiled and typed it in, maybe all was not lost.

Jack sat at the other side of the desk and watched her. He had missed her he acknowledged to himself. He knew he was being pretty nasty to her but it hurt and he was struggling to get past that. Jack wiped his hand over his face, 'we need to get this rubbish sorted, then get time for ourselves, I can't go on much longer like this'

Sam pulled him from his thoughts "That's interesting" she said looking over at him. "Your e-mail seems to be routed through an address registered to a building in Georgetown. It can be accessed from there and changed if necessary."

"Do you have the address?"

"Yeah here" she wrote it down "wait that's not the only thing. You're supposed to be top level security right"

"Yeah" Jack said

"Well it just looks kind of easy, as if someone has deliberately changed your settings"

"How do we find out?"

"Not sure, probably best to deal with the address and then look back at this"

Jack was beginning to get anxious; he needed to be doing something before any disaster came.

"Right time to call in the cavalry or the marines in our case" he said then reached over her to the intercom button on the phone.

"Sgt McIntyre get me the President then General Blake, tell them this is urgent"

"Yes Sir" she replied

Sam and Jack waited less than a minute, then the phone rang "Sir it's the President" McIntyre announced.

"Mister President I'm calling to brief you on a situation" Jack began

"Yes General Landry called, have there been any developments?"

"Sir I would like permission to send some marines to an address in Georgetown. Hopefully minimum civilian impact but if my hunch is correct we should catch a big fish"

"Do I take it that you know who is behind this and their plan?" The President asked

"Not exactly Sir but my gut is telling me we are likely to arrest one of the Ba'al's"

"You have a go" Hayes stated before ending the call.


	11. Chapter 11

Authors Note: Here is chapter 11. Sorry I missed yesterday, two chapters to make up for it. Enjoy

Depending on your point of view the day had either been a complete disaster or a very successful mission.

From his ship in Earth's orbit Ba'al had to confess that this had not been his finest hour. He had not predicted that O'Neill would secretly go to Atlantis and within 3 days blow almost the entire operation. He had underestimated him. He did not like to admit, and certainly would not do so out loud, but in his head he could calmly acknowledge O'Neill had outmanoeuvred him. At least on the Earth side of the operation. There was still hope for controlling Atlantis.

Ba'al, despite the trappings of a God, had learned early that you had to, at least on your own, review where you had gone wrong. The mission had been progressing well. His contacts at the Pentagon, the SGC, Atlantis and his ship were all reporting success up until 36 hours ago. He had heard a few days ago that O'Neill was going away, fishing. He had not been concerned, in fact had scorned at such a primitive pastime. However his SGC and Pentagon contacts had failed him. They had not done enough to ensure that O'Neill was under surveillance. He had only been made aware of the possibilities of problems when he had been unable to reach his SGC contact, Lieutenant Anderson, however he had not realised the full scale of the attack against him.

The incompetent Sgt from the SGC had given him some tale of woe which had befallen Anderson, he should have realised that the broken leg was a false story. Thinking back he understood that there was more to the phone call. The Sgt had been taking his time, trying to uncover information about the caller, undoubtedly to allow someone to track his call. Taking that information on board, he now agreed that the two contacts had failed him

Not only had one been caught but they did not inform him of O'Neill's true travel intentions. He assumed that if the strange Sgt had known of Anderson's deception then Anderson was being punished enough. Fortunately Ba'al had not trusted him with much of the plan, he had been the one to divert mail and had forged the fake letters but apart from that he knew little, in fact all he knew was his God's name.

The other one of these problems, another person that had failed him, was going to be dealt with now.

The day had been disaster but could always be made a little brighter with some torture.

He pressed a button and in a flash his Pentagon contact was standing before him.

"My Lord" the contact bowed

"You have failed me" Ba'al responded

"I am not privy to the minds of those whom I spy on" the contact boldly replied

"Do not talk back to your God"

"I am sorry my Lord, I humbly ask for forgiveness, for a chance to redeem myself"

"I do not grant forgiveness, as for another chance I do not trust those who fail me"

Ba'al flicked a switch and the contact was pulled backwards towards a web similar to the one O'Neill had been on.

"You were given a position to serve your God. You managed with the small tasks of sending e-mails and letters but you have failed when given a more defined role"

"My Lord" the female squeaked

"You do not answer back, you were supposed to be my eyes and ears. You failed me"

"Master"

"You are here for my pleasure since my day and plans were ruined"

As he began the torture and the contact's screams echoed through the ship Ba'al reviewed the day's events. The marines, those arrogant SGC personnel, had stormed into his house. They had not been quiet or discreet but had rushed in to the building. He had no time to destroy the computer evidence or the records he had created. He had been fortunate that his full plan existed only in his head or things would be much worse now. He had stepped into the circle in his attic as O'Neill stood in the door shooting at his personal shield. With a brief salute to him he had activated the rings and ended up here on his cloaked ship.

His musings had obviously increased his anger and bettered his aim as he discovered his contact, the lovely Sgt McIntyre, was already dead.

Although he had a sarcophagus he really did not feel inclined to use it. Instead he summoned his First Prime.

"Deal with that!" he ordered

The Jaffa lifted his zat and zatted the corpse, although dead it still had to be shot 3 times to disappear.

"Where do you wish to us to travel now my Lord?"

"Follow the other ship to Pegasus, there is nothing left for us here"

"As you wish my Lord"

Ba'al looked out the window as Earth disappeared. Yes he may have lost today but the war was not yet over.


	12. Chapter 12

Authors Note: Part 2 of the Jack/Sam conversation. I hope I have done this ok. Have been constantly sorting it and have decided just to post it.

Jack sat in the conservatory at the back of their Washington home. Sam sat in the family room

It had been a couple of days of endless meetings for them both and they had hardly seen each other. Jack had been left in shock by the disappearance of Sgt McIntyre. She had been his aide for two years. He assumed she had worked for Ba'al, there was no official proof although Sam pointed out that she was the likely candidate for downgrading his security settings. He just couldn't believe she was a traitor, but because of her he had geeks all over his office checking to see what she had been working on. How much damage had she been able to cause? Jack was sick of sitting being interrogated by shrubs who had no respect for him or the two stars he now wore. Fortunately, now the President had realised that there was nothing else to discuss in D.C. He had given Sam an extra day to sort herself before redeployment and both Jack and Sam needed to plan what would happen next in their lives. Their professional lives would be all but mapped out, however it was their personal ones that needed discussed.

Unfortunately neither wanted to be the one to make the first move. Both were afraid of what the conversation would bring and ultimately whether they would choose to stay together. They had been sitting in this position for almost an hour, with neither moving to get closer to the other.

Eventually Sam gave in and she walked through the house to the backdoor.

"Jack we need to talk before I go back"

Jack stiffened at that, he hadn't been sure she would go back or, if he was honest, he wanted her to go. The President and the Joint Chiefs had yet to make a plan for Atlantis, given this latest threat.

"I suppose" he said, not wanting to give too much away

"Okay, I'll start. I'm sorry about John"

He looked over at her and noticed the guilty look on her face. However he didn't flinch, sure she was sorry but there was so much more that needed discussed.

"It happened only once, I promise. I was lonely, I missed you and he was just there"

"What…" Jack began, he cleared his throat unsure at whether to ask the question.

She looked at him expectantly

"What would have happened if Daniel hadn't arrived, and please be honest. I would rather know than go on wondering" he had turned to stare at the garden

"Honestly, I don't know. Most of my brain was going to stop me but I won't deny there was a little part of me that knows if we hadn't been in my office I would have gone further"

Jack kept his back to her, he wasn't sure what to think. He never thought Sam would be that honest or want to go that far.

He had to give her credit she was putting all her cards on the table. Well he thought, might as well get back to those plasters he had started on Midway.

"Sam we worked together for 8 years, you never did anything like this for me. Is John worth throwing your career away on?"

Sam turned sharply towards him and pulled at his arm. She had no real idea whether she was talking to Jack or the General and she needed to find out.

"Jack before we do this" she said as calmly as she could "I need to ask something, who is having this conversation?"

"What are you talking about Carter" he said sarcastically, emphasising her name.

"That, that is what I am talking about. Who is here, Jack the man I love or General O'Neill the CO I report to" she stated getting exasperated. This was really not going well

Jack thought through her statement, she was right, he couldn't expect her to do this if he kept flipping from Jack to General depending on how she answered the questions.

"Jack is here, Sam and Jack. General O'Neill already decided not to report you back on Midway"

"Oh" she responded "well I didn't kiss you before, because I didn't want to spoil us, what we might be. I kissed John because for once my brain wasn't in charge of my actions. I hadn't slept in a ridiculous amount of time and I know that has happened before but you have no idea the strength you gave to me just by being in my life. Once you were gone I had nothing to hold on to, nothing to keep me strong or make me sane. For 10 years I had that in some form and when it was taken from me I collapsed, maybe not physically but emotionally I was destroyed. I'm sorry Jack, I didn't mean too and I can't take it back but I need you to forgive me"

"No……" he sighed turning back to the garden.

Sam felt as if her heart was going to break into a million pieces. She moved back towards the house. She reached for her keys in her pocket and took his house key off it. She placed it on the wooden table and quietly said "I'm sorry Jack, I gave up on us, I didn't mean to but I'm sorry, goodbye"

Jack hadn't fully comprehended what was happening but as he turned he saw her head in the door and spotted the key. He then heard her climb the stairs. He reviewed the conversation in his mind. She was leaving, she was leaving now.

He moved out of the garden and ran up the stairs. He caught her just as she was coming out of their room. She was crying. He had a momentary thought. 'this must be bad, Carter never cries, Oh crap'

"Sam wait, I didn't mean I couldn't forgive you. I just…… I just think we both need to clear the air a bit first, please don't leave"

At that moment Sam decided she couldn't take much more. She had been on an emotional rollercoaster for a month now and quite frankly had been a wreck for over a fortnight. This was the last straw. She snapped, dropping her bag on the floor she launched at him.

"'we have to clear the air' 'you have questions' well lets just get started and maybe you can begin to see this from my point of view. For crying out loud Jack, I kissed him once, a month after I found out we had split up and 2 weeks after I believed you were going to be a father, the one thing I can't give you, so forgive me if I for 2 minutes took a step out of reality"

By the end her anger had dissipated and she looked at him totally dejected.

Jack wanted to hug her, tell her it was all fine, but he couldn't. He needed to know other things, make her understand but he could see that he had forgotten how she would feel. How would he have reacted if he had received the letters? Would he have rushed to Atlantis and made her choose him or would he have quit, moved to the cabin and accidentally gone missing in the woods somewhere? Yup, likely. Ok time to build a small bridge

"Sam I'm sorry. It was just a shock. I always expected us to end with you finding someone else so when I saw you both I just assumed……"

"assumed what" she asked

"assumed you would choose him over me" he finished

Sam looked at him, it was always the same, always the elephant in the room. He fully believed she would leave him, mind you going on recent behaviour he had reason to doubt.

"Jack how often do we have to have this conversation? I have chosen you. I chose you a long time ago" She said forcibly

"Oh" he said

"So what else do you need cleared up"  
He shrugged, she had pretty much covered his questions.

She took his silence as an invitation.

"I need to ask about the letters" she moved back into the bedroom and Jack followed her. They stood on opposite sides of the bed, she turned away from him needing to clarify her thoughts.

"the man in the letters, he resented my career, he wanted a baby more than anything" she said quietly

"I can't stop being who I am, I won't be able to have kids easily, you know that and I can't stop being a Colonel. I need to know if you are like the man in the letters, deep down, I need you to be honest"

"Sam I'm useless at this" he said pleading her not to go further with this

"Please Jack, if you want there to be an us after today please try"

"Sam" he spoke quiet but forcefully "I love you, the woman, the geek" he smirked "and the soldier. I could never want you to be less than you are"

He felt this was going better than expected. Just tell her what you feel he thought, the situation can't get any worse.

"What about kids" she asked still not facing him

"Honestly, I would love to be a dad again. I would be absolutely terrified but I would want it"

Sam began to turn towards the door and her abandoned bag "Then maybe you need to find someone who can give you that" she said, her mind made up that Jack deserved better than her.

"Wait Sam, I don't want just any kids. I would only want yours, and I know that's not likely. So if the choice is you or kids I choose you every time" he said gently walking towards her and turning her to face him.

"You do. Why?"

"Sam you are everything to me, no matter where you are you belong with me and that's all I need"

Sam let tears fall down her cheek again. In the last 3 years he had got better at this, but that speech was a minor miracle she thought.

"Do you want to belong with me" he asked hesitantly "cause I would understand if you don't, too much baggage, too many miles on the clock"

"Yes Jack I do belong with you, just like you belong with me"

"Yeah I do" he confirmed

She smiled up at him for the first time since their return from Atlantis "so have we cleared the air enough" she said cheekily.


	13. Chapter 13

Authors Note: Ok here is chapter 13 and we are nearing the end. I know it is short but I will post again tomorrow. This just sets up the ending.

Dr Stephanie Wilder Smythe was an extremely intelligent woman, if she did say so herself. She had arrived on Atlantis to do a job. The people there had no idea. They were weak and completely clueless. Her Lord would destroy them. She had watched them all closely over the last few months.

Mackay believed he could solve anything, how arrogant. However he had not found the beacon she had installed on her arrival and he had yet to realise that she had changed the sensors so they would not see a Goa'uld mother ship. Yes he would pay for his arrogance.

Then there were the military commanders, Colonel Sheppard and the great Colonel Carter. Both were supposed to be unstoppable. They would be shown.

It annoyed Stephanie immensely that Carter had left. She should be here to experience Stephanie's plan. Stephanie had received orders from Ba'al to make it special for Colonel Carter as punishment for O'Neill's annoyance. However she could not be blamed if Carter had left.

The plan was progressing nicely. She had worked through the night to set up the Wraith attack. The program was in place to contact herself instead of Earth when they asked for orders to leave. All Stephanie needed was the final order from Ba'al to proceed.

She locked herself in her quarters ensuring that the door could not be opened by anyone and the cameras were not recording. She knelt down and pulled the small grey ball from under her bed. I had been decided that it was too risky for her to have a large face to face communicator, so the small voice activated ball had to suffice.

"My Lord" Stephanie spoke to the ball

"Are plans progressing" Ba'al responded

"Yes my Lord, we are actually ahead of schedule. Atlantis is not due to be contacted for another 6 days, do you wish to proceed earlier than planned?"

On his ship speeding towards Pegasus Ba'al considered the idea. This would seem to be the perfect solution. He just needed to check a few more details.

"Have there been any visitors to Atlantis recently" he enquired

Stephanie began to blush and in instinct was almost about to kneel in penitence before the ball, she caught herself in time.

"No visitors my Lord, not since SG1 and O'Neill came and Colonel Carter left. I offer my humble apologies my Lord. I was away from the city and unaware of developments until all was finished"

"You are forgiven. I know of others who were at fault"

Ba'al thought for another few moments

"Begin the plan now, launch the Wraith attack in two hours. I will inform the other ship"

"Very well my Lord, all is set up here I will begin immediately"

Stephanie made her way through the quiet corridors of Atlantis. She acknowledged the personnel she passed so as not to make anyone suspicious.

Moving slowly she entered the control room. This was the riskiest part of the plan. All other computer work could be done from her lab but now the program had to be enacted through the main controls.

She looked around – one technician, just as she had suspected. These people had no concept of security or protection.

"Sgt I need to complete part of a system diagnostic I started earlier, could you get me some coffee?"

Stephanie had learnt early on that the easiest way to deceive was to never actually lie, she had started a diagnostic, commenting to random people that she would need to return to finish it. Oh they were just all too gullible.

She quickly enacted the program and step one was accomplished. Midway could no longer contact Atlantis.


	14. Chapter 14

The day after Ba'al had been missed in Georgetown Jack got in touch with General Landry telling him to contact Atlantis and warn them to be on the lookout for trouble. At one of his many meetings he had pointed out that informing Landry was the sensible course of action. It had really worried him that it took over an hour for the D.C. shrubs to agree to his request. Due to the other meetings and trying to convince people that he was not a traitor he had not heard directly from Landry since. It came as a bit of a surprise to Jack when he was rudely awoken that morning by a call from the man himself.

Jack quickly jumped out of bed so that Sam would not be woken and walked down the stairs with the portable phone. After asking after them Landry informed him he had contacted Atlantis and had spoken to a Dr Smythe. He then said that Rodney and John had to leave Atlantis to help Teyla. Jack knew Sam would not like the sound of that, however Landry was satisfied the Dr would keep an eye out, she had been recommended for the position by the President himself. Speaking of which he had a phone call to make.

After he put the phone down for a second time Jack set about making breakfast for them but one look in his cupboard told him he would be better running to the local shop. Once he got back and started on the eggs and pancakes he went to check on Sam. She was just getting up and Jack let himself get momentarily distracted by her. She was beautiful, brilliant and his, totally his, he really thought that up until last night he had not fully believed that. Despite this albeit large blip, she wanted him, wanted to make a life with him.

They had talked again in the middle of the night, Sam was convinced she would need to do more to earn his forgiveness and again Jack had surprised her.

"_Sam I learned a long time ago that you can't earn forgiveness. It has to be given for free. I love you, you did hurt me but the only other option is not to have you in my life and that's not an option" _

_She had burst out crying at that one and Jack, despite feeling bad that he made her cry, had given himself a pat on the back. He was getting better at this, he smiled smugly._

"_But I need to make it up to you, I did something that hurt you" she had continued to push, not believing him_

"_He had sat up at that point and tried to sort out his jumbled thoughts. He might as well tell her the ideas he had, then she would understand_

_No. Sam when Charlie died I spent a long time trying to work out how I could make it up to him and to Sara. She showed me that forgiveness was nothing to do with me and everything to do with her. She had to not blame me."_

"_I am glad you sorted things out Jack but this isn't the same"_

"_Sam I could kick you out, destroy your career, move to the cabin by myself but I don't want any of that. I love you and you made me see how hurt you were by the letters and I don't blame you. You don't need to do anything, I don't want a relationship based on who owes someone something. Like I said before I belong with you and you belong with me. Now can we get back to enjoying being together? Please??_

_Ok so he wasn't above begging. Fortunately she was happy to oblige._

Once he had pulled himself from his memories of the night before Jack reported the conversation with Landry to Sam. She had agreed Stephanie was more than capable of keeping a watch although she had been very annoyed that her base commanders had disobeyed the only order she had given them.

Jack left Sam to change and once they were both sitting at the kitchen table, Jack dropped his next bombshell "So I have been thinking"

"Oh" she was unsure of his tone "I thought we talked through everything last night?"

"We did but I think we need a bit of time to talk without one of us being in another galaxy"

He could see she was about to protest or even worse, get into a state over her career and its impact on 'them' he continued quickly

"So I spoke to the President, he said since you were here we should take some personal time. In his words 'you two have saved the world to often not to get any time for anything else'"

The President had actually added something about a wedding and getting an invite but Jack decided neither of them needed that sort of pressure at this point.

"He said that" Sam responded incredulously

"Yup, so you up for a spot of fishing"

"I think I could cope with that"

"Good cause we are leaving in about an hour, President's jet and all. He must really like us" Jack said with a hint of unbelief in his voice.

They moved quickly around the house, packed and then headed for Andrew's, both looking forward to their first real vacation in almost 2 years.

They boarded the small Lear jet and were soon cruising over Pennsylvania on their way to Minnesota.

Around an hour into the journey things were going well. They were riding in a very comfy plane piloted by two of the air force's finest. The plane had everything Jack could want in a ride. A couple of long couches, big enough for him to sit at one side while Sam had her head on his thigh and read her magazine, definitely the right size. There was a mini-bar, fully stocked, which he had been told was there for their use with no extra charge, excellent. And finally, although this could be the best, neither of the people on board had any idea who they were, saluting got old really quickly in D.C. so this was fantastic. However all good things had to come to an end and Jack covered his face when there was a call from the cockpit.

"Ah Sir, sorry to interrupt but its General Landry, he says it's important"

"Ask him to clarify important Major"

"Yes Sir" the Major responded

A few minutes later he spoke again

"The General says its end of the world important, but I don't have the clearance to be a go between" He repeated the General's words a little sceptically.

"Oh for crying out loud" Jack murmured as he moved to the front of the plane.

The co-pilot came to the back letting Jack have his seat. He wasn't sure what to do so tried to make himself useful tidying up a little. He moved around the area surreptitiously looking at the female passenger.

'These people must be real important' he thought 'President's plane, General calling for them, but they are not wearing uniforms, who could they be'

"So you folks off on holiday" he tried to make conversation

"Yes, first for a long time" Sam replied looking up from her scientific magazine.

The woman seemed friendly and was willing to talk. Captain Franks had always been curious, he knew he shouldn't but he had to ask more

"You both in politics, friends of the President?"

She looked up at him and giggled a little "no not in politics"

Then deciding to take pity on the Captain in case he made a huge mistake without realising it, she added "General O'Neill works at the Pentagon, I work at Cheyenne Mountain, I'm Colonel Carter"

The young man nearly knocked himself out on the overhead storage when he jumped to attention.

"I'm sorry Ma'am, I meant no disrespect, I wasn't told who we were flying" he stuttered through the sentence.

"At ease Captain" she stated leisurely "We like to fly under the radar sometimes"

"Yes Ma'am" he responded just as Jack appeared.

The Captain saluted, and then almost lost his balance as the plane shuddered a little in mid-air. It took all of Sam's training to stop her from giggling.

Jack just breezed past the poor Captain, who returned to the cock-pit. Jack looked over at Sam and she could tell by his look that they were not going on holiday anymore.

"So Colorado or Nevada?" She questioned

"Colorado" He said without missing a beat "We seem to have lost contact with your command"

"With Atlantis" she finished in a whisper, aware of ears in the front of the plane

"Yup"

"Oh how did we find that out?"

"Well it seems you have ole Doc Lee to thank for that. He was trying a new doohickey on Midway and he did something wrong, Hank didn't give details but I imagine he almost blew it up or something. Anyway he tried to contact Mackay and couldn't get through. He thought it was just a glitch so did a system check and still couldn't reach them. He got in touch with the SGC and Landry thinks that Ba'al might have got his plan to work."

AN: so our rollercoaster takes us back to Atlantis. More tomorrow, hopefully.


	15. Chapter 15

Authors Note: I apologise for missing yesterday, therefore two chapters today. Enjoy

Rodney Mackay had tried to stop the team going after Teyla. He had made his case with logic and evidence and had been totally overruled, despite the fact that he was supposed to be in charge. Fortunately his constant planning, organisation and pointing out the obvious had not been fully required, but always better to be safe than sorry.

The team, with Teyla, arrived back on Atlantis to find it in a state of turmoil. There was a Wraith fleet on its way. Both Rodney and John moved into the control room to take over command; John desperate to use military tactics to secure victory, Rodney keen to explain the worst case scenario. As they worked to establish Atlantis' defences things kept going from bad to worse.

One idea after another didn't work and Rodney was running out of them. The shield wasn't working and the cloak couldn't get enough power. The final idea, a radical one at that, was to move Atlantis. As Rodney ran the idea through his head it seemed to get better and better. This could be the solution to their problems. They could fly Atlantis to a new planet and then re-establish contact with Earth. He just had to convince John that the idea had merit.

John, however, was not going to do something as drastic without contacting Earth. Watching from the sidelines Stephanie could not believe how well her Lord had planned this. Even from afar he had managed to control the situation. John would put the call through soon, she would need to be in her quarters to intercept it and give the order. She had managed to rig the gate dialing computer to go through her console before activating the gate. All she had to do was send the wormhole to somewhere other than Earth and no-one would be any the wiser.

Suddenly, and alarmingly for Stephanie, the Stargate started to light up. This was unexpected Atlantis was unable to be contacted from Midway. It had to be direct from Earth, this could not be good.

The worm-hole formed and Jack, Sam, Daniel and Teal'c walked through.

"Hey kids, how's it going?" Jack's irreverent voice could be heard above the panic.

"General O'Neill, Col Carter, it's good to see you all" John said

"We are in the middle of a serious crisis" Rodney added. He didn't normally like to admit he needed help but with Sam he was learning they worked well together.

"Ok lets go to my office" Sam took control.

The group including Stephanie moved to the office where it was standing room only by the time Teal'c and Daniel arrived. Looking round the room Jack took a backseat to Sam in the conversation.

"Ok fill me in" said Sam, immediately silencing Mackay with a look and turning to John for the military perspective, something Jack was immensely grateful for.

"Around 12 hours ago we detected a fleet of Wraith ships coming towards Atlantis. Since then we have tried everything to protect the city but we are running out of ideas. Everything we have tried didn't work and they are now very close. Our latest idea was to contact Earth to get permission to move the city to a safer location" John finished.

Sam thought for a moment and looked at the female Dr.

"Ok, Stephanie did you get the message from Landry" Sam asked

"Yes" she quickly replied "but this is the Wraith not the Goa'uld"

"She's right Sam" Daniel added "Even Ba'al wouldn't get in bed, so to speak, with the Wraith"

"What are you talking about" Rodney asked, more frustrated that he was not included than anything else.

"A lot has happened in the last few days but the main point is Ba'al might be trying to take control of Atlantis" Daniel answered

"We actually thought it had happened, that's why we are here" he continued

"_Did you reach Jack and Sam" Daniel asked as he walked into Landry's office at the SGC._

"_Yes, we decided to wait before contacting Atlantis. They will be here in 2 hours"_

"_Jack wants to be the one to stop Ba'al"_

"_Yes, is there something I need to know about the history here?"_

"_Nothing that is not in the reports. He just always wants to be the one to screw up Ba'al's day"_

"_Well when they arrive you have a go. General O'Neill wants it to be a small operation. If you are walking into a trap he doesn't want any extra casualties"_

"_Well that's nice of him, do we get a choice?" Daniel said jokily _

"_I thought SG1 did things together – all for one?" Landry laughed back_

"_I suppose Teal'c and I can't let them have all the fun. I'll go and tell Teal'c and get organised. Thank you Sir"_

"You thought we had been taken over by a Goa'uld" Rodney asked incredulously

"No not taken over, just under threat" Sam said calmly glaring at Daniel

"What are the pro's and con's of moving" Jack asked from the sidelines pulling the discussion back to the real problem. He might have been leaving the discussion up to the others but everyone knew that ultimately the decision to go or not would be his.

Rodney began to answer the General's question, looking as if he had forgotten Jack was there.

"Well we go, hopefully the Wraith can't trace us and follow us and we find somewhere new"

"Hopefully?" Jack restated, not sounding convinced.

"Sir" John addressed the General "nothing is working to defend us here, the shield won't stabilise and the cloak won't work. We are sitting ducks if we stay"

Stephanie could not have put it better herself, but she needed to keep her cover so added "but if we go, surely these issues will still exist"

"Rodney have you tried everything, a full diagnostic, checked the main computer, strapped someone to the chair to give it commands" Sam interjected.

"Yes everything and nothing works, I don't even know if we will fly"

"We need to make a decision" John began "the Wraith are heading straight for us and will be able to attack in 2 or 3 hours. We are running out of options"

"Ok everyone back to your posts" Sam ordered, the discussion with so many people was getting them nowhere "The general and I will discuss things further, Teal'c, Daniel can you stay as well"


	16. Chapter 16

The four original SG1 members sat in Sam's office contemplating their non-existent options.

"I believe it would be wise to leave" stated Teal'c "We would then have an advantage over the Wraith" he added

"I agree with Teal'c" stated Daniel. "Once we are in hyperspace we can go over things, try to fix them but we will be away from here"

Sam was really wanting Jack's opinion. She valued it over any other but at the moment he seemed reluctant to voice one.

"Sir" she enquired, using his title to show who she wanted to speak to "what do you think?"

Jack looked over at that point, sighed and ran his hand through his hair

"Honestly I have a bad feeling about this. It's all too much of a coincidence and you all know how I feel about those. I mean Ba'al planning an attack, then the Wraith I just don't buy it"

Sam had learned to trust Jack's gut as he would call it. The feeling inside had got them out of trouble many times before.

"But how Jack" Daniel jumped in "We know from interviewing Lieutenant Anderson at the SGC that Ba'al has sent a ship to attack Atlantis, Ba'al is not going to work with the Wraith, but it's them who are coming"

"Says who" Jack stated and Daniel rolled his eyes

"Stop being dense Jack, the computers that's who"

"Yes" said Jack triumphantly turning to Daniel "but the last time I was here the computers had told Carter we were finished. Look we know Ba'al was controlling my office through the Sgt, he had Anderson in full control of mail at the SGC, we were lucky Walter and Hank caught him before he could warn Ba'al. If he has all that in place why can't he have someone here? The computers are telling us nothing is working, I'm no geek like Mackay but how is that possible before an attack" He directed the question to Sam as he turned towards her desk.

Sam looked at both of them. They were right. Jack was right. No-one had seen the Wraith only the computer.

She logged on to her work station as the others looked towards her. Right enough the computer said Wraith but if her e-mail had been tampered with, why not something larger.

She moved out of the room "Rodney" she called leaving the three men to watch her back retreat. "switch everything off, totally I mean everything"

"We tried this" he looked up at her

"alright, alright" he responded to Sam's glare and the one from O'Neill he could see over her shoulder

Sam could sense Jack behind her and turned to him

"Watcha thinking Carter" he drawled

"Not sure, just let me run with it and see what we get"

"Okay, I have confidence in you" she smiled gently at him

"Jack I need you to try the chair now that everything is switched off. The ZPM should still allow you to power it. I need you to do it discreetly. Like you said if the computers have been tampered with someone here did it" she spoke quietly ensuring that she could not been seen or heard by anyone in the control room.

"Right well" Jack replied louder than she had spoken "Teal'c this looks like geek central, how about you and I go and check weapons and defences"

The pair left almost strolling, causing no eyes to follow them.

A few minutes later the chair was activated.

"lets look at that shield first" Jack said, sitting back in the chair.

Back in the control room Mackay was jumping around anxiously. "Colonel something is happening, the shield has just come on line, now the cloak is activated and ready to use once we take the shield down."

"What's going on that's not possible, it wouldn't work when we tried before I swear" John stated

"I know" Sam said calmly "it was just a hunch, our systems must be interfering with it, General O'Neill is powering the chair. There is no 'Earth' technology interfering. I imagine when you tried the chair before you left on some of our systems, security, power to the gate, life support? Once everything was down the chair could function freely"

Seconds later the power went out again and Jack arrived back in the control room.

"So the city still has life" he said stating the obvious

"And there's a great view to the outside, you know I hate those pesky coincidences Carter and it turns out I'm right, no Wraith fleet, only a Goa'uld mother ship, wonder who could have sent that?"

Rodney looked around "but how, a fake fleet you would need to install a programme here, take control of the defences. It had to be someone in the city"

No-one had noticed Teal'c move around the room waiting for someone to break under the pressure. He saw the flicker of movement just before Dr Smythe tried to run and caught her.

"I believe she is your culprit Col Carter"

"Leave me alone, it's not true" responded Stephanie

"It can't be her" John said completely thrown by this "she's one of us"

Rodney however had allowed his mind to mull things over

"but she got the message from Landry and didn't tell us, she was running a diagnostic for days without being told to do one, she was the one who found the fleet, it has all revolved around her" he said aloud

"Teal'c search her quarters, go with him John, see if you can find anything that would back up the accusations" Sam quickly decided.

She looked at Stephanie who looked scared and defiant, Sam really didn't believe this.

"Stephanie for now I am placing you under arrest"

Stephanie looked at her, her face changing to an expression of derision

"It does not matter what happens to me, my Lord will be here soon, you will all bow before him or die"

"Oh brother" O'Neill said and looked around "Is this not getting a little old for anyone?"

Stephanie was taken away by Major Lorne.

"Ok so what do we do now" Daniel asked.

AN: Only one chapter left. Hopefully will post tomorrow. Let me know what you think.


	17. Chapter 17

Jack could get used to this; he was back in the field, fighting the Goa'uld, working with Daniel, Teal' c but most of all working with Carter. Sure it was a little odd, who was giving the orders, who was following them. He was a General, she was the commander of the base but mostly he loved every second of it.

Sam and Rodney had spent the hours following Stephanie's arrest trying to wipe her program from the system. With no success. Every time they booted up the computers they declared nothing worked and the Wraith were coming. The only hope of the city being saved rested with Jack working the chair. His gene was stronger than John's and therefore he had more control.

Normally Jack liked long odds for success but he usually preferred to fight with a P90 or a ZAT, not a chair. He did not do sitting patiently very well.

Sam shut down the computers for the last time and decided they would have to go with Jack especially since he had spotted another mother ship approaching on the long range censors.

The first ship would be within weapons range in a few minutes. Sam realised she had to put the cities fate in Jack's hands. She was a little freaked at that. Of course she trusted him with her own life but now she had to entrust hundreds of lives under her command to him. She knew deep down he could do this or would die trying. However the last time he had done anything like this with Ancient technology his mind was Ancient and then he had to be frozen. So she had issues over the whole thing, irrational issues that were not even worth voicing but issues nonetheless.

Jack and John went down to the chair room. Teal'c joined them, the time had come.

"Sir" Sam spoke through the earpiece "we might only get one shot at this, make it worthwhile"

"Don't worry Carter it's in the bag" Jack said trying to calm her

Jack sat back in the chair, concentrated, located the ship and fired. Ba'al's attack ship disappeared from the radar.

"Direct hit Colonel" John reported to Sam

"Congratulations General" She replied back heaving a sigh of relief

Jack sat up after studying the radar maps "The other ship has turned and has gone back, I think we did it" he said

Everyone was delighted, Jack could hear the cheering from where he was. However in the chair room there was an oppressive atmosphere developing.

Jack sat back in the chair and discreetly nodded his head at Teal'c indicating for him to leave John and him alone.

Teal'c raised his eyebrow to enquire if this was a wise course of action.

Jack simply nodded in return.

Jack looked at the younger man trying desperately to find a way to avoid the coming conversation. However he had decided on the plane to Colorado that if he saw John he would talk to him. Otherwise, if Sam stayed, his imagination would go nuts the whole time she was on Atlantis.

"General, permission to speak freely" John said looking at his superior and instinctively knowing what they were about to talk about.

"Go ahead" Jack said relieved that John was going to start.

"Well Sir I would like to apologise for _aahh_ kissing Colonel Carter the last time you were here. It showed disrespect to Colonel Carter, the uniform and you Sir. You have my word that it had never happened before and it will never happen again"

Sheppard finished, looking at his superior officer for his reaction. There didn't appear to be any.

"Aaahh Sir, if I may ask do you plan to write a report about this, like it deserves"

"No Sheppard, you are right it does deserve it but I already made that decision. The visit wasn't official, it was unexpected, Jack came on holiday with his friends to see Sam. General O'Neill stayed on Midway. I' m here to talk to you as Jack not your boss" He really thought he should get a couple of name badges so that everyone knew who was talking.

"OH" was the only reply Sheppard could formulate.

Jack continued "Sam and I thought you have a right to know what happened. You are about to become one of the few people in the Program that know this, we would appreciate it if it went no further" They had discussed this on the flight. Sam wasn't too happy at his plan to talk to Sheppard but had finally agreed to this.

"Yes Sir"

"Sam and I have been together for a few years. We were never together when we were at the SGC. We got together when we were far enough out of the chain of command. The President knows, and he appointed her to be head here before he asked my opinion so there was no favouritism."

"I never thought there was Sir"

"Anyway" Jack continued "a couple of months ago it seems Ba'al started to mess with people's heads. He effectively split up 8 couples including Sam and I using fake letters and e-mails. When Sam kissed you…" oh he felt really uncomfortable saying that. "she believed I was with someone new, getting married and going to be a father" he stopped

"So that's why she was so sad" John surmised

"Yeah, look Sam is a very private person and we don't want any of this to become city wide gossip" Jack said sternly, irrationally angry that John knew how Sam had been feeling when he had no idea.

"I understand Sir" John said and then continued

"Sir, if I may ask, is she planning to stay?"

Jack looked at the younger man and for the first time since coming to Atlantis for this visit realised that he really did have nothing to fear.  
"I think so, Sam has never run away from a challenge in the 11 years I have known her. Mind you I would prefer her to stay on Earth but I would never hold her back"

John looked slightly shocked at that admission.

"Sir if I may continue to speak freely, why don't you visit more? It must have been well over five months since you have seen each other. Everyone else who has a partner back home gets time off every month or the partner comes here if they are at the SGC it is part of their agreements. Although there have been less recently, oh that was Ba'al's plan" John said finally putting the pieces together, he continued "Why have you not come?"

As soon as he finished John wondered if he had said to much and was about to apologise when he saw the pained look on Jack's face

"Sam didn't want me to come, she was worried what people would think, if it would undermine her authority. Very few people know about us, she didn't want that number to increase" he really needed to stop this conversation, why was he still talking again?

"Sir now that I am aware, you have my word that if you come a reason can be found, heck the fact you work the chair better than anyone is bound to be good for a couple of visits."

Jack smirked at that "The thought had crossed my mind."

"Sir you said earlier that Jack is here not the General, why not let Jack visit and leave the General. No-one here is likely to comment on your relationship. No-one else in your position is apart as much."

Jack was beginning to get back in control of his emotions and for once his mouth that had said way more than he had planned.

"I'll take that under advisement thanks Sheppard, lets get back or Sam will think I've killed you."

The deadpan serious way he said it showing he really could have done that without a second thought gave John the shivers.

In the control room Sam and Rodney had finally managed to get the computers to listen to them and were wiping Stephanie's program from it. Jack and John made their way into the room

"Well Carter, I believe that our work here is done" Jack said with a twinkle in his eye

"Well done Sir" she replied

"You know it is really a shame that we finished this without getting to shoot ole Bocce" he said quite irreverently.

"Can you picture his face now though, his whole plan thwarted by us meddling kids" Daniel piped up

"Indeed" Teal'c answered causing the others to stare at him, unsure he actually knew the television reference

"I was introduced to Scooby Doo by a very excitable Cassandra Frasier many years ago. I find it strange yet enjoyable" Teal'c explained

"Well boys we have saved the day" Jack said to Daniel and Teal'c and then looked at Sam

He could see the concern wash over her face as she moved toward him.

"Are you leaving now?" she asked uncertainly

"Well that depends, can we talk in your office?"

She nodded and they both moved towards the office and sat down, one on either side of the desk.

"So, I talked to John" Jack started "are you planning on staying here?" To Sam the question seemed a little out of left field but Jack really wanted to know what she wanted for her life.

Sam looked down and didn't meet his eyes

"I want to finish my tour Jack, I have a job to do. You know that"

He nodded

"I was sent here for a year with the option to keep going" she paused and took a breath. "I don't think I want to stay after that. She finally looked up at him and held his gaze

He was smiling

"So that would mean you would be back in 3 months then?" He asked wanting to ensure they were on the same page

"Yup"

"Cool, so about me staying for a bit. You know I worked incredibly hard to organise the trip for me and the boys. It would be a shame to go home without celebrating our birthdays"

"With everything that has been going on I forgot it was my birthday" she said with a wistful laugh

"Well Carter, we will just have to remedy that" he stood up from the desk and was about to leave her in peace then turned back to look at her;

"John had some interesting thoughts about me visiting you, how maybe Jack could visit while the General stays home. Maybe it's time to come out of the closet a little bit" he asked warily focusing on her eyes to check her reaction.

After a moment to think she finally responded "Yeah I think this might be the right time" she smiled a little at him

"Ok, well its official I'm on holiday, I think it's time for a spot of fishing, how about it Carter"

They sat on a pier at the outskirts of the city much like they did in Minnesota both lost in their own thoughts.

"Jack, when I get back how about we do something about our undefined relationship"  
"What did you have in mind" hoping he knew what she was hinting at having mentioned it before her job here.

"Well if the offer still stands I would really like to get married"

He smiled, "Whatever you want Sam, whatever you want".

Authors Note: Well here we are at the end of my first major story. Thanks to all who read and especially those who reviewed. It meant a lot. I have others to share with you but they will take a bit to get organised. Hope you enjoyed the ride and that it finished to your satisfaction.


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